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A Practical Guide to Phylogenetics for Nonexperts
Published on: February 5, 2014
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SPECTRE: a suite of phylogenetic tools for reticulate evolution
Sarah Bastkowski1, Daniel Mapleson1, Andreas Spillner2
1Earlham Institute, Norwich Research Park, Norwich NR4 7UZ, UK.
Bioinformatics (Oxford, England)
|November 30, 2017
Summary
SPECTRE is a new open-source Java library providing robust implementations of algorithms for computing split networks, a generalization of phylogenetic trees. This library facilitates the integration of phylogenetic network methods into analysis pipelines and supports advanced computing environments.
Area of Science:
- Computational Biology
- Bioinformatics
- Evolutionary Biology
Background:
- Phylogenetic trees are limited in representing complex evolutionary histories.
- Split networks offer a more generalized framework for visualizing evolutionary relationships.
- Existing software implementations may lack flexibility for advanced users and pipeline integration.
Purpose of the Study:
- To introduce SPECTRE, an open-source Java library for phylogenetic split network computation.
- To provide robust and extensible implementations of split network algorithms.
- To facilitate the integration of phylogenetic network methods into computational workflows.
Main Methods:
- Development of a Java-based library (SPECTRE) for split network data structures and algorithms.
- Implementation of pre-published algorithms for split network construction.
- Inclusion of a graphical interface for visualizing planar split networks.
- Provision of command-line interfaces for server and High Performance Computing execution.
Main Results:
- SPECTRE offers a readily available, open-source solution for computing split networks.
- The library includes new implementations of established algorithms.
- SPECTRE supports both interactive visualization and batch processing for large-scale analyses.
- New implementations of algorithms for computing split networks are provided.
Conclusions:
- SPECTRE enhances the accessibility and usability of split network methods in phylogenetics.
- The library empowers researchers to customize and extend existing phylogenetic network approaches.
- SPECTRE is suitable for diverse computational environments, from desktops to HPC clusters.
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